Season 2: Episode 21 - Zero Day

Zero Day: It's been 10 days since the machine gave Finch and Reese a new number, and the countdown timer on the Stanton Virus is now below the 24 hour mark. After hours of digging and coding, Finch has determined that the virus is using a targeted DDoS attack on the machine to force it to shut down and restart. They finally get a new number, which leads them to the mysterious Ernest Thornhill, a millionaire CEO of a data entry firm, and they go to investigate. Thornhill's company consists of a handful of office drones entering computer code from dot matrix printouts, which Finch finds very strange, and no one appears to have ever met Thornhill in person. Finch digs even deeper and discovers that Thornhill doesn't exist as a real person, but is actually a product of the machine's survival instinct. In other words, Roger Thornhill IS the machine, and the machine is in danger. Reese goes to "Thornhill's" registered apartment, where he runs into Shaw, who is in town tracking Root, but he's taken into custody when police storm the apartment after being tipped off by Finch. Meanwhile, Root blackmails Finch into telling her exactly what will happen when the virus overwhelms the machine and it reboots, so that she can save it from falling into the hands of Decima operatives. Finch explains that the machine will search for a new admin by calling a specific public telephone in the New York Public Library, and Root wants to take that phone call to gain control. Aided by Shaw, Reese escapes police custody and locates Finch at the library, taking out the Decima operatives awaiting the machine's call. Just as the machine reboots, Root takes the call... but Finch manages to send a second call to a phone near Reese, who picks up the receiver and answers...
Carter, meanwhile, is faced with a flood of new cases. The virus' stranglehold on the machine has prevented Reese from halting murders and violent crimes, and the crime rate is up nearly twenty percent. However, when Detective Terney informs her that he has a lead on Detective Beecher's killer, she drops everything to go with him. They arrive at the location where the suspect is, and just when it looks like Terney is going to shoot Carter in the back, an armed Russian thug runs out of the building, forcing Carter to shoot him. Later, she is stunned to learn that the gun the thug was carrying has mysteriously vanished, and that Internal Affairs thinks it was an unmotivated shooting. Carter slowly realizes that she's been set-up...
In flashback, we see the happier days of Finch's relationship with Grace, including the day he decided to ask her to marry him. The happy couple is contrasted with Finch's crumbling relationship with his former partner, Nathan Ingram, who built a backdoor into the machine's code without Finch's knowledge. That backdoor provides Ingram with the "irrelevant numbers" -- the numbers that Finch and Reese currently use. Finch is furious with Ingram for his tampering and decides to reverse the code, shutting the irrelevant list down just as Ingram's own number comes up on the screen. Unfortunately, neither Finch nor Ingram see it.

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